Research workbench
Crystal structure of PURO/IMP from methanothermobacter thermoautotrophicus
Analyse Crystal structure of PURO/IMP from methanothermobacter thermoautotrophicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NTK
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imp cyclohydrolase
- EC
- 3.5.4.10
- UniProt
- O27099
- Ligands
- IMP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imp cyclohydrolase (EC 3.5.4.10) | protein | 206 | 20% helix, 40% strand | O27099 |
| B, C, D | Imp cyclohydrolase (EC 3.5.4.10) | protein | 202 | 21% helix, 41% strand | O27099 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.77 | 0.82 | 67 | empty |
| 2 | 786 | 0.76 | 0.80 | 64 | empty |
| 3 | 99 | 0.54 | 0.84 | 20 | IMP |
| 4 | 84 | 0.51 | 0.84 | 19 | IMP |
| 5 | 90 | 0.50 | 0.83 | 20 | IMP |
Interfaces
6 interfaces between chains.
- B–C · 874 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 817 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 663 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 661 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 299 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2NTK · Crystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus · the same entry in another collection · chain A against A, TM-score 1.00
- O27099 · AlphaFold monomer V2.0 prediction for imp cyclohydrolase (O27099) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O27099
- Elsewhere: RCSB PDB 2NTK · PDBe 2NTK · UniProt O27099
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